The Lost Companion
by Empress-Anna
Summary: She had been trapped in the TARDIS for a very long time. She finally finds a way out but loses her memory. Now the Doctor must help her regain her memory to find out what she was doing in the TARDIS to start with. I'm sorry I suck at summaries the story is a lot better. Rated T for minor bad language. Some spoilers for Doomsday.
1. The Story Begins

**Disclaimer I do not own Doctor Who, that honor goes to BBC. And Steven Moffat.**

**All reviews are welcome if you think the doctor is out of character please tell me.**

**J**

The Doctor had for gotten her. She was trapped in one of the rooms. But this room only had one door, and she couldn't reach it. How long had she been in here? The TARDIS had helped her when she could. She had food at least. But she couldn't leave, she had started thinking she was going mad. She kept seeing him, she would see him reaching down from the door wearing his leather jacket and with his ridiculously large ears. "Come on." He would say. And she would reach up only to see him dissolve back into the dream he was.

There she was, trapped in the TARDIS. She had finally had it. Today she was determined to get out. What made her so determined? She had forgotten her name. She had forgotten who she was, where she was, and what she was waiting for. She ran at the wall opposite of her, kicked off it, twisted in mid-air 'till at long last she gripped the frame of the door and hauled herself through it. She was in a maze of hallways and doors, not caring where she went, she ran. She ran as fast and as far as she could, away from the horrid room she had lived in for so long. She was free it was finally hitting her.

She soon came across a vast room with a strange sort of mechanical desk with a tube coming out of the center of it. The sides of the room were lined with strange columns. She got the feeling that the room was alive and watching her. At the mechanical desk was a tall slender man wearing a pinstripe suit and white trainers. His hair was sticking out like he had been running his hands through it. She decided it was best not to let him see her. She snuck past him hiding behind the columns as she made her way to the door. Silently she pleaded for him not to see her. However she was not so lucky. She was almost to the door when he turned. She quickly hid behind one of the columns.

"Is somebody there?" he spoke loudly as if he were talking to a deaf person. She stayed silent crouching behind the column only too aware that she was in an uncomfortable position. She tried to shift just enough to ease her discomfort. His eyes flew to the column she was hiding behind. "Come out, I promise not to hurt you." His voice was softer now, kinder, with a hint of sympathy that she couldn't remember hearing before. Part of her wanted to move out of her hiding place and reveal herself, but most of her wanted to stay hidden. For all she knew this man had kidnapped her and locked her in that God awful room. So she stayed hidden hardly daring to breath. He walked over and sat on the railing. "You can come out. I'm not going to hurt you."

God! Why did he have to speak like that? His gentle, soft, soothing voice made her want to run out and hug him.

"Why are you hiding?"

She wanted to melt into that voice, to give in, but she knew she couldn't. She couldn't even tell him her name.

"Who are you?"

God! Why did he have to say that? She let out the breath she hadn't realized she was holding.

"Are you all right? Can you talk?"

She couldn't stay here and it was clear he knew she was there. She decided to make a break for the door. Not letting herself change her mind she took off for the door. He caught her by the waist. In her panic she screamed.

"NO! LET GO OF ME! LET GO!" He gently placed her on the ground and turned her to face him. He put his hands on her shoulders to ensure that she couldn't run off.

"Alright. Okay." His voice was almost a whisper. She tried to pull away from him but he held her shoulders firmly. "How did you get here?" he said. She just glared at him. "Come on, say something. What's your name?"

She squirmed not meeting his eyes. "You don't remember, do you?" It sounded more like a statement than a question. "Do you remember anything?" His voice had dropped to a whisper. His question echoed in her head. She closed her eyes trying to remember but all she got was a hand and a cry to run. She opened her eyes and looked up at him meeting his eyes. His eyes were like nothing she had ever seen. Somehow they were gentle yet threatening both wonderful and horrifying at the same time. They seemed so much older than the rest of him. This was a person who had seen too much. However she could tell despite everything else that he cared. She instinctively stepped back from him and his eyes. He loosened his grip but didn't fully release her.

"Come on. I'll make you a cuppa tea." He wrapped one arm around her shoulders and started to lead her back the way she had come. She suddenly remembered the room and stopped. "What's wrong?"

She didn't speak she refused to meet his eyes even when he stood in front of her. "Are you alright?" She closed her eyes. When she didn't open them after a while he asked "Why won't you open your eyes?"

She let a small smile show as she thought of several funny retorts to what he had just said. Then she found his hand on her arm and gently squeezed it before opening her eyes. She smiled to convince him everything was fine. He gave her a look before leading her down the hallway. When they got to the kitchen she sat down desperate to get out from under his arm. If it bothered him he didn't say anything. He handed her a cup of tea then sat next to her. She swirled the tea in the cup without drinking any. "Not thirsty?"


	2. Talking to The Doctor

**I just realized i didn't put what she is wearing. It's an orange dress with a fox tail and exposed stomach. She is also wearing a mask and has ginger hair.**

**Please review. I like reviews reviews are good.**

She placed the cup on the table then buried her face in her arms and started laughing silently. She heard the man move suddenly and places a hand on her back. "Are you okay?"

All she could do in reply was nod. She could not remember anything so she really shouldn't be laughing, but it just bubbled forth in an extreme amount of joy. Eventually the laughter subsided, she sat up to see him looking at her with a curious expression on his face. "Why are you laughing?"

She couldn't tell him the truth even she didn't know. "You still haven't told me your name." She said with a chuckle. He smiled and said "I'm the Doctor, hello."

She stopped laughing and closed my eyes as a memory surfaced.

_There was a man. He looked almost 40 and he had abnormally large ears and a leather jacket. He was talking. "I'm the Doctor."_

The memory faded.

"No you're not."

"Yes I am. Why do you think I'm not the Doctor?"  
>"I met him at least once. But he was older and short hair almost like a military cut. He also had really large ears and wore a leather jacket."<p>

"I'm him. But I don't remember you. Why?"

"I could ask the same question."

"But you just said you know me."

"No I said I knew the Doctor…sort of, but what I meant was, I don't remember me."

He looked sad she decided to change the subject. "If it helps the TARDIS might know something I have been here a long time."

"How did you know my ship is called the TARDIS?"

"I don't know but I do know that when the Doctor thought he was alone he called her Sexy."

"Who are you?"

"I don't know."

"How did you get amnesia?"

"I don't remember."

"Alright come with me."

"Where to?"

"The Medical Bay." She followed him without a word. All the while trying to remember who she was. Then an odd question entered her mind.

"When did you regenerate?"

"What?"

"How did you regenerate?"

"How did yo…"

"If you really are the Doctor then you must have regenerated since I last saw you."

"I absorbed the time vortex to save my friend?"

"Where is your friend now?"

"Gone."

"I'm sorry. What was their name?"

"Rose. Her name was Rose."

"Nice name. Was she nice?"

"Yeah."

They walked in silence for a little while. The Doctor broke the silence. "How did you know I regenerate?"

"I don't know."

"What do you know?"

"N- Wait hang on was that an insult?"

"No! What can you remember?"

"Not a lot." She said softly looking away to hide the tears threatening to fall. "I'm sorry." He said after a little pause.

"It's okay. I'll beat you up later." She managed to give him a smile before looking back to the ground. He placed a hand on her arm. She ignored it, she hated being touched but didn't want to offend him. "Hang on, why do you think the TARDIS will know?"

"I've been here a long time. She took care of me."

"Took care of you how? How long have you been here?"

"She fed me. I'd say I've been here days at least."

"Days?"

"At least. It's hard to keep track."

"Well the TARDIS does tend to have that effect."

"Don't you have a security camera or something?"

"I used to."

"Great. So there's no hope." She said plopping down on one of the beds in the Medical Bay.

"I didn't say that." She looks at him. "I've been stuck here for God knows how long, with no memory of how I got here, how long I've been here, and I don't even know what caused my memory loss. Not to mention I have random questions and words pop into my head. Did I miss anything?"

"Okay it does sound a bit bad when you say it like that." She scoffs. "A bit?"

"Tiny bit. But we'll figure it out. I promise."

"I hope so. It's bugging me." He started scanning her. "How old are you now?" she asked suddenly. "904"

"Really? You don't look that old."

"I'm not human."

"I kinda figured that out. Humans don't regenerate."

"For someone with amnesia you seem to know a lot about me."

"I don't understand it any more than you do." She said closing her eyes as another memory surfaced.

_The Doctor grabbed her hand. "Run!"_

_"Why? Where are we going!" she yelled as he pulled her along._

Her eyes flashed open and she jerked back. "Are you okay?"

"Y-yeah."

"You sure?"

"It's just memories trying to come back."

"What did you remember?"

"The Doctor telling me to run."

"When did I tell you to run?"

"I don't know and I'm still not convinced you are the Doctor."

"Why not?"

"You don't look like him, you don't sound like him, you don't act like him, and you have no clue who I am."

"But I am him. There could be something keeping me from remembering you."

"Answer me this. If you are the Doctor than what is his real name?"

"I don't tell anyone my real name and even if I had told you, you wouldn't remember it."

"Worth a shot." She smiled, leaned back and closed her eyes.

_"Why are we running?"_

_"You were surrounded by Vashta Narada."_

_"I was surrounded by what?"_

_"Living shadows. They kill."_

_"Oh. Okay then." They ran for a while before stopping outside a blue police box. "We are being chased by living shadows and you are fiddling with an old police box?"_

_"Trust me."_

_"I don't even know you." He pulled her inside._

_"Whoa!" She said as he closed the door behind her. "Okay. I'm dead. Dead or dreaming."_

_"You're not dead."_

_"Then I'm dreaming."_

_"No. Do you want me to pinch you?"_

Her eyes opened again. He was looking at her curiously. "What's Vashta Narada?"

"Living shadows. Is that what you were running from?"

"What?"

"Were you just remembering running from the Vashta Narada?"

"Not sure. Are you done yet?"

"Just about."

"Ugh wake me when it's over."

"Why. Do you not want to stay awake?"

"I'm bored."

"Well. I'm done now."

"Finally. Can I go to sleep now?"

"You tired?"

"A bit." She proved it by yawning. He helped her off the bed. "Just so you know I will not sleep in the Medical Bay."

"I wasn't going to make you."

"So did the medical scanny thingy tell you anything?"

"First you need some sleep then we will discuss your health." She stuck her tongue out at him, he didn't notice. "I'll find you a room." He said leading her down the infinite hallways. She followed him nervously.


	3. Not Alone

**Due to a time issue involving school and work I may be slower in updating. However I will keep working at it and update as soon as the chapters are typed. Thank you to all who have read, followed, and/or reviewed. It is very much appreciated. **

He led her to a simple wooden door. "You can sleep in here." He said opening the door. Inside was a twin sized bed with a dark oak frame. The colors of the room reminded her of something but she couldn't remember what. Everything was orange and red. She walked around the room and discovered a simple bathroom and a walk-in closet. "So do you like it?"

"I love it." She said smiling. "If you want to lock me in here I'll understand."

"Why would I want to do that?"

"I'm a complete stranger who knows you and suddenly standing in your TARDIS. I wouldn't trust me. I don't expect you to trust me."

"Nah. If you had planned to do anything you wouldn't have said anything about locking you in." She smiled at him. He turned to walk out. "Where is your room?" He turned back. "Don't worry about it. I'll be in the console room."

"Where's that?"

"Uh. That way." He said pointing. She walked over. "Okay." She said after looking in the direction he was pointing. He smiled at her, then closed the door.

She was alone. She was glad of it. He weirded her out. Just a little. Sighing she plopped down on the bed. She felt like two different people when she was around him. One was completely terrified of him. The other adored him. Not in the romantic sense, more like a good friend sort of way. She didn't know what to do, and that frightened her.

_She was running through the TARDIS. She had to get away. God knows where the Doctor was. She didn't know how it had gotten in here, but it was after her. It was right behind her, closing in. "Hide me." She thought. Silently begging the TARDIS for help. The ground opened underneath her and she fell._

She awoke with a cry. She realized where she was and sat up. She sighed and walked to the bathroom. She splashed cold water in her face just as a knock sounded at the door. "What is it?" She yelled to him. "Are you alright? I heard a yell."

"Yeah."

"Can I come in?"

"Not right now. I can meet you in the console room in a little while."

"Are you sure you're alright?"

"Still sleepy but other than that I'm fine."

"Ok. I'll just wait in the console room then."

She could picture him standing outside the door deciding whether he should sonic the door or not. She decided to see if he was. "You still out there?"

"Yeah." She laughed. "You do know I'm gonna be a while."

"Yeah."

"I'm indecent. Don't try to get in." She lied. "Okay." She heard him walk away. She guessed he was going to the console room. She laughed again before deciding to shower.

When she got out of the shower she looked in the mirror. She was startled by her appearance. She was almost grey in skin color and her cheeks and eyes were hollowed out. From what she could see with the mask still on her eyes had dark circles. The worst of it was she was covered in scars. She didn't know why she hadn't seen them before.

She pulled herself away from the mirror. It was then that she noticed the outfit on the side of the sink. She guessed the TARDIS had left it for her. It was an orange dress. It matched her ginger hair. She smiled whispering a 'thank you' before putting it on. It had a fox tail sewed onto the back. There was also a mask that matched it. It looked like a fox's face. She hid her face as she replaced her old mask with the new one. She couldn't remember why but she knew no living thing could see her face.

When she was finished she walked to the console room. She found him staring at a screen. He didn't look up when she walked in.

She crept up behind him to see what he was looking at. It was a scan of her. She could see both her hearts in it. "What cha looking at?" She said loudly. He jumped then turned around to face her. "What are you?"

"I'm sorry?"

"What species are you? What is your planet?"

"Human, Earth. Why?"

"No you're not human. Try to remember what you are."

"I'm human. Of course I'm human. Why wouldn't I be?"

"You are currently speaking Gallifreyic. I turned off the translator."

"I'm speaking what!?"

"Gallifreyic the language of the time lords of Gallefry."

"Time Lords?"

"It's what I am. Apparently it's what you are too."

"No, I'm pretty sure I'm human."

"You have two hearts and you are speaking the language of the Time Lords." He pointed at the screen he had been looking at when she had walked in. "See two hearts."

"I know I have two hearts. What makes you think I'm speaking Gallefryic?"

"You know you have two hearts?"

"Yes some humans have two hearts."

"Really?"

"Yes about 5 humans on earth have two hearts. It's a rare genetic disorder. And don't go saying they're aliens because I know two of them and their mothers and they are pure blood human."

"Well that may be true, but you have Time Lord DNA as well."

"And you still haven't answered my question."

"What wa- Oh! Because I turned off the translator so we shouldn't be able to understand each other unless we were speaking the same language."

"Oh makes sense I suppose. But I am still completely confused. Hey what is that blank spot right there?" She said pointing at the screen. "Should something be there?"

"I haven't figured that out yet."

"Great so I have a hole in my chest."

"Not necessarily it could be some kind of machinery hidden by a perception filter."

"So basically you're saying I'm Borg."

"You're what?"

"It's a Star Trek reference."

"What's _Borg_?"

"I'd say the closest thing to a Borg that you would recognize would be a cyberman. They assimilate anyone who they think they could use. Instead of upgrade."

"Oh. You know about cybermen?"

"Yes."

"Why did you yell?"

"I was dreaming."

"About cybermen?"

"No. Maybe. I don't know. Something."

"You didn't see it?"

"No. I yelled because the ground disappeared beneath me."

"Why did the ground disappear?"

"How would I know?"

"It was your dream."

"That doesn't make me the dream genius." She almost yelled in her frustration. "Sorry." He turned back to the screen. She felt bad. She stepped up and hugged him from behind. "Why are you hugging me?"

"Don't know. Just wanted to." She felt him laugh, she couldn't help but smile at him. She let go of him and stepped back. He turned to face her. "We should go somewhere, I'm getting cabin fever." She said still smiling. "Is it contagious?" She laughed. "No it just means I'm bored and cooped up. I mean the TARDIS is huge and all but it's still inside and I need to see some form of sunlight."

"Any idea as to where you want to go?"

"Somewhere quiet." She said remembering the dream. "Try to avoid places where we will have to run." He turned and started pushing buttons. She watched him set the course of where they would be going. She knew the TARDIS had a mind of her own and if she wanted them somewhere then she would put them there. She hoped there wasn't any worlds or ships that needed saving. She needed time to think. She instinctively grabbed the railing when he pushed the lever that would set them on their way. Despite her dizziness and the turbulence she managed to stay upright.


	4. Jigzanzi

**Okay so sorry about the wait. I had a lot of school work to do but mostly caught up now. And a shout-out to my cousin KR. This chapter is a bit quiet due to the excitement I plan for the next chapter.**

"So where are we?"

"Jigznanzi."

"Okay. Can I go outside?"

"After you." She turned and ran towards the door. She suddenly turned around. "You won't leave me here will you?"

"Nah. Wouldn't think of it." She smiled, opened the door, and walked outside. The sky was violet-orange with three moons. They had landed in a meadow of gold grass that reflected the sky. She heard him step out behind her. "It's not inhabited in this continent yet."

"Anything dangerous that I should worry about?"

"No, there's no insect life, no dangerous animals, and no poisonous plants."

"So the perfect world then."

"Yeah. So whatddya think?"

"It's beautiful." She frowned as a memory surfaced. Just flashes this time. She saw a forest that looked like fire, at sunset. The face of an old man and a young girl with white hair.

"You alright?" His voice shattered her thoughts. She looked up at him. "Yeah. Just thinking."

"Oh what about?"

"Not sure yet. I'll let you know when I figure it out." She walked forward and lay down in the gold grass.

She heard him walk up behind her and looked up at him. He took his coat off and sat down on it. "I love purple." She said after he sat down. "Really I'm more of a blue person."

"I never really liked blue. Hurts my eyes. 'Course I like red even though it does the same thing." She closed her eyes. "What 'bout purple?"

"Not really. Just sensitive to blue, red, and white. Some sounds too. And don't say that's weird."

"Wasn't going to." She looked over at him. He flashed her a lopsided grin. She let out a small laugh. The sun disappeared over the horizon. "You'll want to watch this."

"What?"

"Just watch." As on cue thousands of gold flowers bloomed. Each releasing a yellow light. She sat up. "Oh! That's gorgeous." She exclaimed. She looked back at him, he still had that goofy grin on his face.

She wrapped her arms around him in a hug. "Thank you." She spoke softly in his ear. He hugged her back. "You're welcome."

"So where is this place?"

"In the galaxy the humans call Andromeda."

"We'll have to come back sometime."

"Maybe we will." He smiled.

"A sudden wave of exhaustion came over her and she closed her eyes. She felt completely safe in the soft glow from the flowers, with him next to her. She could tell now that he was the Doctor. There was no doubt about it, only the Doctor would care this much for a stranger. She fell asleep.

**I know this is a short chapter but with Thanksgiving break starting tomorrow and being unable to update at home I decided to publish what was typed. Please review, or PM me let me know what you think. Her story will come to an end soon, if you like the story and want a sequel please tell me. :)**


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